The human genome harbors about one million interspersed repetitive sequences and many gene families, affording a myriad of opportunities for illegitimate recombination which can generating deletions, duplications, translocations and other genetic rearrangements, as well as reduction to deleterious homozygosity in mitosis. Yet mammalian genomes are remarkably stable. Are there specific molecular mechanisms in mammals and other higher eukaryotes that impede illegitimate recombination or mobile element transposition? Experiments with E. coli indicate that formation of heteroduplex recombination intermediates can be aborted due to the presence of only a few mismatches. Studies of Neurospora and Ascobolus suggest that repeated sequences are preferentially methylated at cytosines, and 5-methylcytosines suffer deamination to thymidine, forming mutational hotspots. Methyl-directed mutation in these sequences has been designated as ripping (repeat-induced point mutations). Thus, divergence between repeated sequences could be generated via high-frequency methylation of cytosine, providing a mechanism to specifically inhibit recombination between multicopy sequences and to inactivate transposable elements by mutation. In higher eukaryotes methylation occurs most frequently at CpG dinucleotides. We are determining by computer analysis whether CpG dinucleotides are less frequent in gene families than in single-copy genes, and whether CpG dinucleotides undergo transition to TpG as would be expected if their cytosine residues were methylated and subsequently deaminated. Additional experiments include cloning and sequencing of polyoma transgenes introduced into mice to determine if ripping occurs when multiple rather than single copies of genes have been introduced. These studies have significance for the expression of foreign genes and targeted mutagenesis in higher eukaryotes and for strategies of gene therapy in genetic disorders.